Problem loading Genome with .json file

[Matthias Habjan]

Dear colleagues,

I want to load a genome that is not available in the IGV desktop version.

I downloaded the .json file here:

http://ftp.ensembl.org/pub/release-105/json/

When I load the Genome I get zero response from the IGV software. Can anyone help and tell me what I am doing wrong?

When I look at the .json file it doesn't look anything similar to what is described here:

https://github.com/igvteam/igv/wiki/JSON-Genome-Format

Appreciate your help

[igv-help]

That is not an IGV json format, as you have noted, I'm not really sure what your question is beyond that.   To load a reference into IGV you need to create a file as specified.   Its best to do this in a plain text editor.

Jim

[Matthias Habjan]

Thanks for your reply Jim. Alright, then I am on the right track at least...

I want to load a genome (fasta) and all annotations into IGV and couldn't manage so far to create a json-file myself. Loading the fasta-file was successful though. But then I will keep trying ;)

[James Robinson]

Yes, just loading the fasta is the simplest way to define a reference.  The json format is really for those who want to share a complete reference + annotations with others.

For annotations you can just load them from the File menu in supported formats (gff3, gtf, or bed).

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